Author: Miguel Jácome-Flores

Chamaerops humilis Bipartite Networks analysis


Frugivores visits


Figure 1. Meles meles tracks in sandtramp beneath a C. humilis infructesence.

Figure 1. Meles meles tracks in “sandtramp” beneath a C. humilis infructesence.

 

Step 1. Open Martinazo and Matasgordas matrix

Opening a matrix file with weighted visits of frugivores in individual plants, the “row.names=1” is necessary to run the model and to detect the “name of plants” in the matrix. Note: visit frequency= animal-visit-days/total-survey days.

#Martinazo
mart<-read.csv("~/Desktop/Palmito/Postdoc-Interaction Networks/mart_visit.csv",header=TRUE,check.names=FALSE,row.names=1)

#Matasgordas
matas<-read.csv("~/Desktop/Palmito/Postdoc-Interaction Networks/matas_visit.csv",header=TRUE,check.names=FALSE,row.names=1)

 

Step 2. Using “bipartite” package

library(bipartite)
Step 2.1. Ploting the web.

Creates a bipartite network were the high level will be represented by the frugivores and low level to each individual plant. Plants arrengement represents the aggregation level from high-low aggregation. This was obtained through Dirilichet tesselations, where plants haighly aggregated were those with the less area without any other dwarf palm. 1

 

Step 3. Calculate different indexes of a network.

  • Closeness scores for nodes in a weighted network based on the distance_w-function.

  • Betweenness scores for nodes in a weighted network based on the distance_w-function.

  • Species level describe a species’ degree as sum of its links.

  • Link level computes the contribution of each species to the overall nestedness.

## Warning in as.tnet(net, type = "weighted one-mode tnet"): There were self-
## loops in the edgelist, these were removed

## Warning in as.tnet(net, type = "weighted one-mode tnet"): There were self-
## loops in the edgelist, these were removed
## This function is SLOW! 
## Monitor your system's activity; depending on steps-setting this may take minutes to hours!
## 
## identifyModules: start building legal dendrogram
## 
## #steps   M   best M  temperature
## [1016]   0.0176224       (-2.06866e-16)      1e-05
## 
## identifyModules: building of legal dendrogram finished
## identifyModules: start finding best dendrogram
## 
## [1016]   0.0176224       (0.0176224)     1e-05
## [10000]  0.0257446       (0.0257446)     9.95804e-06
## [20000]  0.240315        (0.240315)      9.99552e-06
## [30000]  0.267135        (0.267135)      9.92285e-06
## [40000]  0.282473        (0.282473)      9.95486e-06
## [50000]  0.284198        (0.284198)      9.94546e-06
## [60000]  0.284198        (0.284198)      9.84567e-06
## [70000]  0.284198        (0.284198)      9.74587e-06
## [80000]  0.284198        (0.284198)      9.64607e-06
## [90000]  0.284198        (0.284198)      9.54627e-06
## [93222]  0.284198        (0.284198)      9.51412e-06
## [100000] 0.284198        (0.284198)      9.44648e-06
## [110000] 0.284198        (0.284198)      9.34668e-06
## [120000] 0.284198        (0.284198)      9.24688e-06
## [130000] 0.284198        (0.284198)      9.14709e-06
## [140000] 0.284198        (0.284198)      9.04729e-06
## [150000] 0.284198        (0.284198)      8.94749e-06
## [160000] 0.284198        (0.284198)      8.84769e-06
## [170000] 0.284198        (0.284198)      8.7479e-06
## [180000] 0.284198        (0.284198)      8.6481e-06
## [190000] 0.284198        (0.284198)      8.5483e-06
## [200000] 0.284198        (0.284198)      8.4485e-06
## [210000] 0.284198        (0.284198)      8.34871e-06
## [220000] 0.284198        (0.284198)      8.24891e-06
## [230000] 0.284198        (0.284198)      8.14911e-06
## [240000] 0.284198        (0.284198)      8.04931e-06
## [250000] 0.284198        (0.284198)      7.94952e-06
## [260000] 0.284198        (0.284198)      7.84972e-06
## [270000] 0.284198        (0.284198)      7.74992e-06
## [280000] 0.284198        (0.284198)      7.65012e-06
## [290000] 0.284198        (0.284198)      7.55033e-06
## [300000] 0.284198        (0.284198)      7.45053e-06
## [310000] 0.284198        (0.284198)      7.35073e-06
## [320000] 0.284198        (0.284198)      7.25093e-06
## [330000] 0.284198        (0.284198)      7.15114e-06
## [340000] 0.284198        (0.284198)      7.05134e-06
## [350000] 0.284198        (0.284198)      6.95154e-06
## [360000] 0.284198        (0.284198)      6.85174e-06
## [370000] 0.284198        (0.284198)      6.75195e-06
## [380000] 0.284198        (0.284198)      6.65215e-06
## [390000] 0.284198        (0.284198)      6.55235e-06
## [400000] 0.284198        (0.284198)      6.45255e-06
## [410000] 0.284198        (0.284198)      6.35276e-06
## [420000] 0.284198        (0.284198)      6.25296e-06
## [430000] 0.284198        (0.284198)      6.15316e-06
## [440000] 0.284198        (0.284198)      6.05336e-06
## [445608] 0.284198        (0.284198)      5.9974e-06
## [450000] 0.284198        (0.284198)      5.95357e-06
## [460000] 0.284198        (0.284198)      5.85377e-06
## [470000] 0.284198        (0.284198)      5.75397e-06
## [480000] 0.284198        (0.284198)      5.65417e-06
## [490000] 0.284198        (0.284198)      5.55438e-06
## [500000] 0.284198        (0.284198)      5.45458e-06
## [510000] 0.284198        (0.284198)      5.35478e-06
## [520000] 0.284198        (0.284198)      5.25498e-06
## [530000] 0.284198        (0.284198)      5.15519e-06
## [540000] 0.284198        (0.284198)      5.05539e-06
## [550000] 0.284198        (0.284198)      4.95559e-06
## [560000] 0.284198        (0.284198)      4.85579e-06
## [570000] 0.284198        (0.284198)      4.756e-06
## [580000] 0.284198        (0.284198)      4.6562e-06
## [590000] 0.284198        (0.284198)      4.5564e-06
## [600000] 0.284198        (0.284198)      4.4566e-06
## [610000] 0.284198        (0.284198)      4.35681e-06
## [620000] 0.284198        (0.284198)      4.25701e-06
## [630000] 0.284198        (0.284198)      4.15721e-06
## [640000] 0.284198        (0.284198)      4.05742e-06
## [650000] 0.284198        (0.284198)      3.95762e-06
## [660000] 0.284198        (0.284198)      3.85782e-06
## [670000] 0.284198        (0.284198)      3.75802e-06
## [680000] 0.284198        (0.284198)      3.65823e-06
## [690000] 0.284198        (0.284198)      3.55843e-06
## [700000] 0.284198        (0.284198)      3.45863e-06
## [710000] 0.284198        (0.284198)      3.35883e-06
## [720000] 0.284198        (0.284198)      3.25904e-06
## [730000] 0.284198        (0.284198)      3.15924e-06
## [740000] 0.284198        (0.284198)      3.05944e-06
## [750000] 0.284198        (0.284198)      2.95964e-06
## [760000] 0.284198        (0.284198)      2.85985e-06
## [769400] 0.284198        (0.284198)      2.76604e-06
## [770000] 0.284198        (0.284198)      2.76005e-06
## [780000] 0.284198        (0.284198)      2.66025e-06
## [790000] 0.284198        (0.284198)      2.56045e-06
## [800000] 0.284198        (0.284198)      2.46066e-06
## [810000] 0.284198        (0.284198)      2.36086e-06
## [820000] 0.284198        (0.284198)      2.26106e-06
## [830000] 0.284198        (0.284198)      2.16126e-06
## [840000] 0.284198        (0.284198)      2.06147e-06
## [850000] 0.284198        (0.284198)      1.96167e-06
## [860000] 0.284198        (0.284198)      1.86187e-06
## [870000] 0.284198        (0.284198)      1.76207e-06
## [880000] 0.284198        (0.284198)      1.66228e-06
## [890000] 0.284198        (0.284198)      1.56248e-06
## [900000] 0.284198        (0.284198)      1.46268e-06
## [910000] 0.284198        (0.284198)      1.36288e-06
## [920000] 0.284198        (0.284198)      1.26309e-06
## [930000] 0.284198        (0.284198)      1.16329e-06
## [940000] 0.284198        (0.284198)      1.06349e-06
## [950000] 0.284198        (0.284198)      9.63694e-07
## [960000] 0.284198        (0.284198)      8.63897e-07
## [970000] 0.284198        (0.284198)      7.64099e-07
## [980000] 0.284198        (0.284198)      6.64302e-07
## [990000] 0.284198        (0.284198)      5.64504e-07
## [1000000]    0.284198        (0.284198)      4.64707e-07
## [1010000]    0.284198        (0.284198)      3.64909e-07
## [1020000]    0.284198        (0.284198)      2.65112e-07
## [1030000]    0.284198        (0.284198)      1.65314e-07
## [1040000]    0.284198        (0.284198)      6.5517e-08
## [1050000]    0.284198        (0.284198)      9.97962e-12
## 
## identifyModules: finding best dendrogram complete
## 
## identifyModules: modularity = 0.284198
## This function is SLOW! 
## Monitor your system's activity; depending on steps-setting this may take minutes to hours!
## 
## identifyModules: start building legal dendrogram
## 
## #steps   M   best M  temperature
## [10000]  -47.9832        (-47.9832)      1e-05
## [20000]  -8.06976e-16        (-5.7067e-16)       1e-05
## [30000]  -1.0087e-15     (-5.7067e-16)       1e-05
## [33411]  -1.03031e-15        (-5.7067e-16)       1e-05
## [39488]  0.00741797      (-5.7067e-16)       1e-05
## 
## identifyModules: building of legal dendrogram finished
## identifyModules: start finding best dendrogram
## 
## [39488]  0.00741797      (0.00741797)        9.98392e-06
## [40000]  0.00741797      (0.00741797)        9.97881e-06
## [50000]  0.0476313       (0.0476313)     9.9302e-06
## [60000]  0.0544581       (0.0544581)     9.91877e-06
## [70000]  0.0544581       (0.0544581)     9.81882e-06
## [80000]  0.0544581       (0.0544581)     9.71886e-06
## [90000]  0.069576        (0.069576)      9.95186e-06
## [100000] 0.069576        (0.069576)      9.85217e-06
## [110000] 0.069576        (0.069576)      9.75248e-06
## [120000] 0.0762916       (0.0762916)     9.93387e-06
## [130000] 0.0762916       (0.0762916)     9.83416e-06
## [140000] 0.18954     (0.18954)       9.95882e-06
## [150000] 0.208527        (0.208527)      9.96025e-06
## [160000] 0.21134     (0.21134)       9.92591e-06
## [165159] 0.272956        (0.272956)      9.98972e-06
## [170000] 0.272956        (0.272956)      9.94136e-06
## [180000] 0.272956        (0.272956)      9.84146e-06
## [190000] 0.275769        (0.275769)      9.91323e-06
## [200000] 0.275769        (0.275769)      9.81327e-06
## [210000] 0.275769        (0.275769)      9.71331e-06
## [220000] 0.340263        (0.340263)      9.9536e-06
## [230000] 0.354702        (0.354702)      9.91666e-06
## [240000] 0.362083        (0.362083)      9.9014e-06
## [250000] 0.362083        (0.362083)      9.80143e-06
## [260000] 0.365619        (0.365619)      9.93917e-06
## [270000] 0.365619        (0.365619)      9.83932e-06
## [280000] 0.365619        (0.365619)      9.73946e-06
## [290000] 0.365619        (0.365619)      9.63961e-06
## [300000] 0.365619        (0.365619)      9.53975e-06
## [310000] 0.365619        (0.365619)      9.4399e-06
## [320000] 0.365619        (0.365619)      9.34005e-06
## [330000] 0.365619        (0.365619)      9.24019e-06
## [340000] 0.365619        (0.365619)      9.14034e-06
## [350000] 0.365619        (0.365619)      9.04048e-06
## [360000] 0.365619        (0.365619)      8.94063e-06
## [370000] 0.365619        (0.365619)      8.84078e-06
## [380000] 0.365619        (0.365619)      8.74092e-06
## [390000] 0.365619        (0.365619)      8.64107e-06
## [400000] 0.365619        (0.365619)      8.54121e-06
## [410000] 0.365619        (0.365619)      8.44136e-06
## [417122] 0.365619        (0.365619)      8.37024e-06
## [420000] 0.365619        (0.365619)      8.3415e-06
## [430000] 0.365619        (0.365619)      8.24165e-06
## [440000] 0.365619        (0.365619)      8.1418e-06
## [450000] 0.365619        (0.365619)      8.04194e-06
## [460000] 0.365619        (0.365619)      7.94209e-06
## [470000] 0.365619        (0.365619)      7.84223e-06
## [480000] 0.365619        (0.365619)      7.74238e-06
## [490000] 0.365619        (0.365619)      7.64252e-06
## [500000] 0.365619        (0.365619)      7.54267e-06
## [510000] 0.365619        (0.365619)      7.44282e-06
## [520000] 0.365619        (0.365619)      7.34296e-06
## [530000] 0.365619        (0.365619)      7.24311e-06
## [540000] 0.365619        (0.365619)      7.14325e-06
## [550000] 0.365619        (0.365619)      7.0434e-06
## [560000] 0.365619        (0.365619)      6.94354e-06
## [570000] 0.365619        (0.365619)      6.84369e-06
## [580000] 0.365619        (0.365619)      6.74384e-06
## [590000] 0.365619        (0.365619)      6.64398e-06
## [600000] 0.365619        (0.365619)      6.54413e-06
## [610000] 0.365619        (0.365619)      6.44427e-06
## [620000] 0.365619        (0.365619)      6.34442e-06
## [630000] 0.365619        (0.365619)      6.24456e-06
## [640000] 0.365619        (0.365619)      6.14471e-06
## [650000] 0.365619        (0.365619)      6.04486e-06
## [660000] 0.365619        (0.365619)      5.945e-06
## [670000] 0.365619        (0.365619)      5.84515e-06
## [680000] 0.365619        (0.365619)      5.74529e-06
## [690000] 0.365619        (0.365619)      5.64544e-06
## [700000] 0.365619        (0.365619)      5.54559e-06
## [710000] 0.365619        (0.365619)      5.44573e-06
## [720000] 0.365619        (0.365619)      5.34588e-06
## [730000] 0.365619        (0.365619)      5.24602e-06
## [734494] 0.365619        (0.365619)      5.20115e-06
## [740000] 0.365619        (0.365619)      5.14617e-06
## [750000] 0.365619        (0.365619)      5.04631e-06
## [760000] 0.365619        (0.365619)      4.94646e-06
## [770000] 0.365619        (0.365619)      4.84661e-06
## [780000] 0.365619        (0.365619)      4.74675e-06
## [790000] 0.365619        (0.365619)      4.6469e-06
## [800000] 0.365619        (0.365619)      4.54704e-06
## [810000] 0.365619        (0.365619)      4.44719e-06
## [820000] 0.365619        (0.365619)      4.34733e-06
## [830000] 0.365619        (0.365619)      4.24748e-06
## [840000] 0.365619        (0.365619)      4.14763e-06
## [850000] 0.365619        (0.365619)      4.04777e-06
## [860000] 0.365619        (0.365619)      3.94792e-06
## [870000] 0.365619        (0.365619)      3.84806e-06
## [880000] 0.365619        (0.365619)      3.74821e-06
## [890000] 0.365619        (0.365619)      3.64835e-06
## [900000] 0.365619        (0.365619)      3.5485e-06
## [910000] 0.365619        (0.365619)      3.44865e-06
## [920000] 0.365619        (0.365619)      3.34879e-06
## [930000] 0.365619        (0.365619)      3.24894e-06
## [940000] 0.365619        (0.365619)      3.14908e-06
## [950000] 0.365619        (0.365619)      3.04923e-06
## [960000] 0.365619        (0.365619)      2.94937e-06
## [970000] 0.365619        (0.365619)      2.84952e-06
## [980000] 0.365619        (0.365619)      2.74967e-06
## [990000] 0.365619        (0.365619)      2.64981e-06
## [1000000]    0.365619        (0.365619)      2.54996e-06
## [1010000]    0.365619        (0.365619)      2.4501e-06
## [1020000]    0.365619        (0.365619)      2.35025e-06
## [1030000]    0.365619        (0.365619)      2.2504e-06
## [1034639]    0.365619        (0.365619)      2.20407e-06
## [1040000]    0.365619        (0.365619)      2.15054e-06
## [1050000]    0.365619        (0.365619)      2.05069e-06
## [1060000]    0.365619        (0.365619)      1.95083e-06
## [1070000]    0.365619        (0.365619)      1.85098e-06
## [1080000]    0.365619        (0.365619)      1.75112e-06
## [1090000]    0.365619        (0.365619)      1.65127e-06
## [1100000]    0.365619        (0.365619)      1.55142e-06
## [1110000]    0.365619        (0.365619)      1.45156e-06
## [1120000]    0.365619        (0.365619)      1.35171e-06
## [1130000]    0.365619        (0.365619)      1.25185e-06
## [1140000]    0.365619        (0.365619)      1.152e-06
## [1150000]    0.365619        (0.365619)      1.05214e-06
## [1160000]    0.365619        (0.365619)      9.5229e-07
## [1170000]    0.365619        (0.365619)      8.52436e-07
## [1180000]    0.365619        (0.365619)      7.52581e-07
## [1190000]    0.365619        (0.365619)      6.52727e-07
## [1200000]    0.365619        (0.365619)      5.52873e-07
## [1210000]    0.365619        (0.365619)      4.53019e-07
## [1220000]    0.365619        (0.365619)      3.53164e-07
## [1230000]    0.365619        (0.365619)      2.5331e-07
## [1240000]    0.365619        (0.365619)      1.53456e-07
## [1247177]    0.365619        (0.365619)      8.17906e-08
## [1250000]    0.365619        (0.365619)      5.36018e-08
## [1260000]    0.365619        (0.365619)      9.98534e-12
## 
## identifyModules: finding best dendrogram complete
## 
## identifyModules: modularity = 0.365619

 

Coping the results to my folder in local repository

write.table(clos_mart, "/Users/apple/Desktop/Palmito/Postdoc-Interaction Networks/Dispersal Networks/clos_mart.txt", sep="\t")

Fruit remotion rates


Figure 2. Wildboar feeding on C. humilis fruits

Figure 2. Wildboar feeding on C. humilis fruits

 

Step 1. Open Martinazo and Matasgordas matrix

Opening a matrix file with weighted links with frugivores fruit remotion in individual plants. Other specifications of the matrix are described in the previous section.

#Martinazo
mart_f<-read.csv("~/Desktop/Palmito/Postdoc-Interaction Networks/mart_fruits.csv",header=TRUE,check.names=FALSE,row.names=1)

#Matasgordas
matas_f<-read.csv("~/Desktop/Palmito/Postdoc-Interaction Networks/matas_fruits.csv",header=TRUE,check.names=FALSE,row.names=1)

 

Step 2. Using “bipartite” package

 

library(biparite)

   

Step 2.1. Ploting the web.

Creates a bipartite network were the high level will be represented by the frugivores and low level to each individual plant. Links are weigthed with the proportion fruit remotion proportion/animal/individual plant.2

Step 3. Calculate different indexes of a network.3

  • Closeness

  • Betweenness

  • Species level

  • Link level

## This function is SLOW! 
## Monitor your system's activity; depending on steps-setting this may take minutes to hours!
## 
## identifyModules: start building legal dendrogram
## 
## #steps   M   best M  temperature
## [3738]   1.52005e-16     (-13.2803)      1e-05
## 
## identifyModules: building of legal dendrogram finished
## identifyModules: start finding best dendrogram
## 
## [3738]   1.52005e-16     (1.52005e-16)       9.99338e-06
## [10000]  0.103459        (0.103459)      9.96394e-06
## [20000]  0.200954        (0.200954)      9.94433e-06
## [30000]  0.203494        (0.203494)      9.88669e-06
## [40000]  0.203494        (0.203494)      9.78707e-06
## [50000]  0.203494        (0.203494)      9.68744e-06
## [60000]  0.203494        (0.203494)      9.58782e-06
## [70000]  0.450592        (0.450592)      9.94106e-06
## [80000]  0.450592        (0.450592)      9.84143e-06
## [90000]  0.450592        (0.450592)      9.74181e-06
## [100000] 0.450592        (0.450592)      9.64218e-06
## [110000] 0.450592        (0.450592)      9.54255e-06
## [120000] 0.450592        (0.450592)      9.44293e-06
## [130000] 0.450592        (0.450592)      9.3433e-06
## [140000] 0.450592        (0.450592)      9.24367e-06
## [150000] 0.450592        (0.450592)      9.14405e-06
## [160000] 0.450592        (0.450592)      9.04442e-06
## [170000] 0.450592        (0.450592)      8.9448e-06
## [180000] 0.450592        (0.450592)      8.84517e-06
## [190000] 0.450592        (0.450592)      8.74554e-06
## [200000] 0.450592        (0.450592)      8.64592e-06
## [210000] 0.450592        (0.450592)      8.54629e-06
## [220000] 0.450592        (0.450592)      8.44667e-06
## [230000] 0.450592        (0.450592)      8.34704e-06
## [240000] 0.450592        (0.450592)      8.24741e-06
## [250000] 0.450592        (0.450592)      8.14779e-06
## [260000] 0.450592        (0.450592)      8.04816e-06
## [262747] 0.450592        (0.450592)      8.02079e-06
## [270000] 0.450592        (0.450592)      7.94853e-06
## [280000] 0.450592        (0.450592)      7.84891e-06
## [290000] 0.450592        (0.450592)      7.74928e-06
## [300000] 0.450592        (0.450592)      7.64966e-06
## [310000] 0.450592        (0.450592)      7.55003e-06
## [320000] 0.450592        (0.450592)      7.4504e-06
## [330000] 0.450592        (0.450592)      7.35078e-06
## [340000] 0.450592        (0.450592)      7.25115e-06
## [350000] 0.450592        (0.450592)      7.15153e-06
## [360000] 0.450592        (0.450592)      7.0519e-06
## [370000] 0.450592        (0.450592)      6.95227e-06
## [380000] 0.450592        (0.450592)      6.85265e-06
## [390000] 0.450592        (0.450592)      6.75302e-06
## [400000] 0.450592        (0.450592)      6.65339e-06
## [410000] 0.450592        (0.450592)      6.55377e-06
## [420000] 0.450592        (0.450592)      6.45414e-06
## [430000] 0.450592        (0.450592)      6.35452e-06
## [440000] 0.450592        (0.450592)      6.25489e-06
## [450000] 0.450592        (0.450592)      6.15526e-06
## [460000] 0.450592        (0.450592)      6.05564e-06
## [470000] 0.450592        (0.450592)      5.95601e-06
## [480000] 0.450592        (0.450592)      5.85639e-06
## [490000] 0.450592        (0.450592)      5.75676e-06
## [500000] 0.450592        (0.450592)      5.65713e-06
## [510000] 0.450592        (0.450592)      5.55751e-06
## [520000] 0.450592        (0.450592)      5.45788e-06
## [530000] 0.450592        (0.450592)      5.35825e-06
## [540000] 0.450592        (0.450592)      5.25863e-06
## [550000] 0.450592        (0.450592)      5.159e-06
## [560000] 0.450592        (0.450592)      5.05938e-06
## [570000] 0.450592        (0.450592)      4.95975e-06
## [580000] 0.450592        (0.450592)      4.86012e-06
## [585570] 0.450592        (0.450592)      4.80463e-06
## [590000] 0.450592        (0.450592)      4.7605e-06
## [600000] 0.450592        (0.450592)      4.66087e-06
## [610000] 0.450592        (0.450592)      4.56124e-06
## [620000] 0.450592        (0.450592)      4.46162e-06
## [630000] 0.450592        (0.450592)      4.36199e-06
## [640000] 0.450592        (0.450592)      4.26237e-06
## [650000] 0.450592        (0.450592)      4.16274e-06
## [660000] 0.450592        (0.450592)      4.06311e-06
## [670000] 0.450592        (0.450592)      3.96349e-06
## [680000] 0.450592        (0.450592)      3.86386e-06
## [690000] 0.450592        (0.450592)      3.76424e-06
## [700000] 0.450592        (0.450592)      3.66461e-06
## [710000] 0.450592        (0.450592)      3.56498e-06
## [720000] 0.450592        (0.450592)      3.46536e-06
## [730000] 0.450592        (0.450592)      3.36573e-06
## [740000] 0.450592        (0.450592)      3.2661e-06
## [750000] 0.450592        (0.450592)      3.16648e-06
## [760000] 0.450592        (0.450592)      3.06685e-06
## [770000] 0.450592        (0.450592)      2.96723e-06
## [780000] 0.450592        (0.450592)      2.8676e-06
## [790000] 0.450592        (0.450592)      2.76797e-06
## [800000] 0.450592        (0.450592)      2.66835e-06
## [810000] 0.450592        (0.450592)      2.56872e-06
## [820000] 0.450592        (0.450592)      2.4691e-06
## [830000] 0.450592        (0.450592)      2.36947e-06
## [840000] 0.450592        (0.450592)      2.26984e-06
## [850000] 0.450592        (0.450592)      2.17022e-06
## [860000] 0.450592        (0.450592)      2.07059e-06
## [870000] 0.450592        (0.450592)      1.97096e-06
## [880000] 0.450592        (0.450592)      1.87134e-06
## [890000] 0.450592        (0.450592)      1.77171e-06
## [900000] 0.450592        (0.450592)      1.67209e-06
## [910000] 0.450592        (0.450592)      1.57246e-06
## [920000] 0.450592        (0.450592)      1.47283e-06
## [930000] 0.450592        (0.450592)      1.37321e-06
## [940000] 0.450592        (0.450592)      1.27358e-06
## [950000] 0.450592        (0.450592)      1.17395e-06
## [959167] 0.450592        (0.450592)      1.08263e-06
## [960000] 0.450592        (0.450592)      1.07433e-06
## [970000] 0.450592        (0.450592)      9.74703e-07
## [980000] 0.450592        (0.450592)      8.75076e-07
## [990000] 0.450592        (0.450592)      7.7545e-07
## [1000000]    0.450592        (0.450592)      6.75824e-07
## [1010000]    0.450592        (0.450592)      5.76198e-07
## [1020000]    0.450592        (0.450592)      4.76572e-07
## [1030000]    0.450592        (0.450592)      3.76946e-07
## [1040000]    0.450592        (0.450592)      2.77319e-07
## [1050000]    0.450592        (0.450592)      1.77693e-07
## [1060000]    0.450592        (0.450592)      7.80671e-08
## [1070000]    0.450592        (0.450592)      8.99335e-17
## 
## identifyModules: finding best dendrogram complete
## 
## identifyModules: modularity = 0.450592
## Warning in as.tnet(net, type = "weighted one-mode tnet"): There were self-
## loops in the edgelist, these were removed

## Warning in as.tnet(net, type = "weighted one-mode tnet"): There were self-
## loops in the edgelist, these were removed
## This function is SLOW! 
## Monitor your system's activity; depending on steps-setting this may take minutes to hours!
## 
## identifyModules: start building legal dendrogram
## 
## #steps   M   best M  temperature
## [2789]   0.118098        (-19.8825)      1e-05
## 
## identifyModules: building of legal dendrogram finished
## identifyModules: start finding best dendrogram
## 
## [2789]   0.118098        (0.118098)      9.99498e-06
## [10000]  0.186527        (0.186527)      9.94492e-06
## [20000]  0.186806        (0.186806)      9.92008e-06
## [26501]  0.256627        (0.256627)      9.96829e-06
## [30000]  0.259395        (0.259395)      9.9788e-06
## [40000]  0.259395        (0.259395)      9.87881e-06
## [50000]  0.259395        (0.259395)      9.77881e-06
## [60000]  0.272373        (0.272373)      9.91845e-06
## [70000]  0.272373        (0.272373)      9.81901e-06
## [80000]  0.326501        (0.326501)      9.93573e-06
## [90000]  0.326501        (0.326501)      9.83616e-06
## [100000] 0.333754        (0.333754)      9.90239e-06
## [110000] 0.358014        (0.358014)      9.95246e-06
## [120000] 0.36687     (0.36687)       9.90931e-06
## [130000] 0.36687     (0.36687)       9.80932e-06
## [140000] 0.36687     (0.36687)       9.70933e-06
## [150000] 0.36687     (0.36687)       9.60934e-06
## [160000] 0.36687     (0.36687)       9.50934e-06
## [170000] 0.36687     (0.36687)       9.40935e-06
## [180000] 0.36687     (0.36687)       9.30936e-06
## [190000] 0.36687     (0.36687)       9.20937e-06
## [200000] 0.36687     (0.36687)       9.10937e-06
## [210000] 0.36687     (0.36687)       9.00938e-06
## [220000] 0.36687     (0.36687)       8.90939e-06
## [230000] 0.36687     (0.36687)       8.8094e-06
## [240000] 0.36687     (0.36687)       8.7094e-06
## [250000] 0.36687     (0.36687)       8.60941e-06
## [260000] 0.36687     (0.36687)       8.50942e-06
## [270000] 0.36687     (0.36687)       8.40943e-06
## [280000] 0.36687     (0.36687)       8.30944e-06
## [290000] 0.36687     (0.36687)       8.20944e-06
## [300000] 0.36687     (0.36687)       8.10945e-06
## [306776] 0.36687     (0.36687)       8.0417e-06
## [310000] 0.36687     (0.36687)       8.00946e-06
## [320000] 0.36687     (0.36687)       7.90947e-06
## [330000] 0.36687     (0.36687)       7.80947e-06
## [340000] 0.36687     (0.36687)       7.70948e-06
## [350000] 0.36687     (0.36687)       7.60949e-06
## [360000] 0.36687     (0.36687)       7.5095e-06
## [370000] 0.36687     (0.36687)       7.4095e-06
## [380000] 0.36687     (0.36687)       7.30951e-06
## [390000] 0.36687     (0.36687)       7.20952e-06
## [400000] 0.36687     (0.36687)       7.10953e-06
## [410000] 0.36687     (0.36687)       7.00953e-06
## [420000] 0.36687     (0.36687)       6.90954e-06
## [430000] 0.36687     (0.36687)       6.80955e-06
## [440000] 0.36687     (0.36687)       6.70956e-06
## [450000] 0.36687     (0.36687)       6.60957e-06
## [460000] 0.36687     (0.36687)       6.50957e-06
## [470000] 0.36687     (0.36687)       6.40958e-06
## [480000] 0.36687     (0.36687)       6.30959e-06
## [490000] 0.36687     (0.36687)       6.2096e-06
## [500000] 0.36687     (0.36687)       6.1096e-06
## [510000] 0.36687     (0.36687)       6.00961e-06
## [520000] 0.36687     (0.36687)       5.90962e-06
## [530000] 0.36687     (0.36687)       5.80963e-06
## [540000] 0.36687     (0.36687)       5.70963e-06
## [550000] 0.36687     (0.36687)       5.60964e-06
## [560000] 0.36687     (0.36687)       5.50965e-06
## [570000] 0.36687     (0.36687)       5.40966e-06
## [580000] 0.36687     (0.36687)       5.30966e-06
## [590000] 0.36687     (0.36687)       5.20967e-06
## [600000] 0.36687     (0.36687)       5.10968e-06
## [610000] 0.36687     (0.36687)       5.00969e-06
## [620000] 0.36687     (0.36687)       4.9097e-06
## [630000] 0.36687     (0.36687)       4.8097e-06
## [640000] 0.36687     (0.36687)       4.70971e-06
## [645832] 0.36687     (0.36687)       4.65139e-06
## [650000] 0.36687     (0.36687)       4.60972e-06
## [660000] 0.36687     (0.36687)       4.50973e-06
## [670000] 0.36687     (0.36687)       4.40973e-06
## [680000] 0.36687     (0.36687)       4.30974e-06
## [690000] 0.36687     (0.36687)       4.20975e-06
## [700000] 0.36687     (0.36687)       4.10976e-06
## [710000] 0.36687     (0.36687)       4.00976e-06
## [720000] 0.36687     (0.36687)       3.90977e-06
## [730000] 0.36687     (0.36687)       3.80978e-06
## [740000] 0.36687     (0.36687)       3.70979e-06
## [750000] 0.36687     (0.36687)       3.60979e-06
## [760000] 0.36687     (0.36687)       3.5098e-06
## [770000] 0.36687     (0.36687)       3.40981e-06
## [780000] 0.36687     (0.36687)       3.30982e-06
## [790000] 0.36687     (0.36687)       3.20982e-06
## [800000] 0.36687     (0.36687)       3.10983e-06
## [810000] 0.36687     (0.36687)       3.00984e-06
## [820000] 0.36687     (0.36687)       2.90985e-06
## [830000] 0.36687     (0.36687)       2.80986e-06
## [840000] 0.36687     (0.36687)       2.70986e-06
## [850000] 0.36687     (0.36687)       2.60987e-06
## [860000] 0.36687     (0.36687)       2.50988e-06
## [870000] 0.36687     (0.36687)       2.40989e-06
## [880000] 0.36687     (0.36687)       2.30989e-06
## [890000] 0.36687     (0.36687)       2.2099e-06
## [900000] 0.36687     (0.36687)       2.10991e-06
## [910000] 0.36687     (0.36687)       2.00992e-06
## [920000] 0.36687     (0.36687)       1.90992e-06
## [930000] 0.36687     (0.36687)       1.80993e-06
## [940000] 0.36687     (0.36687)       1.70994e-06
## [950000] 0.36687     (0.36687)       1.60995e-06
## [960000] 0.36687     (0.36687)       1.50995e-06
## [970000] 0.36687     (0.36687)       1.40996e-06
## [980000] 0.36687     (0.36687)       1.30997e-06
## [990000] 0.36687     (0.36687)       1.20998e-06
## [996440] 0.36687     (0.36687)       1.14558e-06
## [1000000]    0.36687     (0.36687)       1.10999e-06
## [1010000]    0.36687     (0.36687)       1.00999e-06
## [1020000]    0.36687     (0.36687)       9.10001e-07
## [1030000]    0.36687     (0.36687)       8.10008e-07
## [1040000]    0.36687     (0.36687)       7.10016e-07
## [1050000]    0.36687     (0.36687)       6.10023e-07
## [1060000]    0.36687     (0.36687)       5.10031e-07
## [1070000]    0.36687     (0.36687)       4.10039e-07
## [1080000]    0.36687     (0.36687)       3.10046e-07
## [1090000]    0.36687     (0.36687)       2.10054e-07
## [1100000]    0.36687     (0.36687)       1.10062e-07
## [1110000]    0.36687     (0.36687)       1.00692e-08
## [1120000]    0.36687     (0.36687)       9.99909e-12
## 
## identifyModules: finding best dendrogram complete
## 
## identifyModules: modularity = 0.36687

 

Step 3.1. Ploting modules in the networks

                                                                         

Step 4. Gathering Martinazo and Matasgordas’ matrixs as one; plants are ordered from more to less aggregated

 

Step 5. Changing the matrix by eliminating unknown visitors

#Martinazo
mart_fnun<-read.csv("~/Desktop/Palmito/Postdoc-Interaction Networks/mart_fruits_no_unk.csv",header=TRUE,check.names=FALSE,row.names=1)

#Matasgordas
matas_fnun<-read.csv("~/Desktop/Palmito/Postdoc-Interaction Networks/matas_fruits_no_unk.csv",header=TRUE,check.names=FALSE,row.names=1)

 

Bipartite plot


  1. Notice: Plants colors in gray scale [col.low=c(gray(seq(0.1,1,length=24)))], goes from black (aggregated plants) to white (more isolated), length refers to the number of plants in the plot. In High level, different colors in “col.high” means different guilds: white=predators, dark gray=defleshers, black=dispersers and light gray=unknow.

  2. For more information see previous analysis

  3. For more information see previous analysis